Security tail wags the dog
BOAC
Has hit the nail on the head about the security aspects of who you should have access to the flight deck.
The security people have written the rues on flight deck access with one narrow aim in mind, that is to protect themselves and their political masters from political problems. Flight safety is not on their agenda.
In this situation a second skilled pair of hands on the flight deck was a very good move and enhanced the safety of the aircraft despite being in direct contravention of the rules.
This is a very good practical example of the saying " the rules are written for the guidance of wise men and the blind obedience of fools".